rs2143417

Variant names:

• chr1-186684655-G-T
• rs2143417

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.218 in 152,048 control chromosomes in the GnomAD database, including 4,658 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.22 (4658 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 16 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33101 AN: 151930 Hom.: 4638 Cov.: 32

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.0493

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.0866

Gnomad MID AF: 0.224

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.221

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.218 AC: 33160 AN: 152048 Hom.: 4658 Cov.: 32 AF XY: 0.213 AC XY: 15820 AN XY: 74346

African (AFR) AF: 0.391 AC: 16200 AN: 41444

American (AMR) AF: 0.186 AC: 2843 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 810 AN: 3468

East Asian (EAS) AF: 0.0491 AC: 254 AN: 5176

South Asian (SAS) AF: 0.164 AC: 793 AN: 4824

European-Finnish (FIN) AF: 0.0866 AC: 917 AN: 10586

Middle Eastern (MID) AF: 0.224 AC: 65 AN: 290

European-Non Finnish (NFE) AF: 0.158 AC: 10732 AN: 67962

Other (OTH) AF: 0.224 AC: 472 AN: 2108

Alfa AF: 0.174 Hom.: 1390

Bravo AF: 0.234

Asia WGS AF: 0.159 AC: 555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.7
DANN	Benign	0.62
PhyloP100		0.35

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2143417; hg19: chr1-186653787;